Related papers: Thermodynamically Driven Signal Amplification
A tight binding model for scanning tunneling microscopy images of a molecule adsorbed on a metal surface is described. The model is similar in spirit to that used to analyze conduction along molecular wires connecting two metal leads and…
Simulation schemes that allow to change molecular representation in a subvolume of the simulation box while preserving the equilibrium with the surrounding introduce conceptual problems of thermodynamic consistency. In this work we present…
Thermodynamic aspects of chemical reactions have a long history in the Physical Chemistry literature. In particular, biochemical cycles - the building-blocks of biochemical systems - require a source of energy to function. However, although…
An important aspect of astrophysical MHD turbulence research is developing diagnostics to connect simulations with the observable universe. Turbulent systems are by definition structurally complex in all fluid variables (density, velocity,…
Living systems operate out of equilibrium, continuously consuming energy to sustain organised, functional states. Their emergent behaviour usually relies on a set of interconnected chemical reaction networks (CRNs) driven by external fluxes…
We analyze the conditions for entanglement amplification between distant and not directly interacting quantum objects by their common coupling to media with static modular structure and subject to a local (single-bond) quenched dynamics. We…
Probabilistic Boolean networks (PBNs) is an important mathematical framework widely used for modelling and analysing biological systems. PBNs are suited for modelling large biological systems, which more and more often arise in systems…
Tethered particle motion (TPM) --- the motion of a micro- or nanoparticle tethered to a substrate by a macromolecule --- is a system that has proven extremely useful for its ability to reveal physical features of the tether, because the…
Due to the limited capabilities of a single bio-nanomachine, complicated tasks can be performed only with the co-operation of multiple bio-nanomachines. In this work, we consider a diffusion-based molecular communication system with a…
We study the role of active coupling on the transport properties of homogeneously charged macromolecules in an infinitely dilute solution. An enzyme becomes actively bound to a segment of the macromolecule, exerting an electrostatic force…
The phenomenon of quantum entanglement underlies several important protocols that enable emerging quantum technologies. Entangled states, however, are extremely delicate and often get perturbed by tiny fluctuations in their external…
Balanced data is required for deep neural networks (DNNs) when learning to perform power system stability assessment. However, power system measurement data contains relatively few events from where power system dynamics can be learnt. To…
The hydrogen trapping behaviour of metallic alloys is generally characterised using Thermal Desorption Spectroscopy (TDS). However, as an indirect method, extracting key parameters (trap binding energies and densities) remains a significant…
Regulatory networks (RNs) are a well-accepted modelling formalism in computational systems biology. The control of RNs is currently receiving a lot of attention because it provides a computational basis for cell reprogramming -- an…
The coupling of two-level quantum systems to the thermal environment is a fundamental problem, with applications ranging from qubit state preparation to spin models. However, for the elementary problem of the thermodynamics of an ensemble…
There is a common view in thermodynamics that the behavior of a macroscopic system can be described by only a few state variables. Although this is true for many cases, it is unclear whether it is meaningful to ask how many state variables…
Machine learning (ML) has become a standard tool for the exploration of chemical space. Much of the performance of such models depends on the chosen database for a given task. Here, this aspect is investigated for "chemical tasks" including…
Considering a broad class of steady-state nonequilibrium systems for which some additive quantities are conserved by the dynamics, we introduce from a statistical approach intensive thermodynamic parameters (ITPs) conjugated to the…
Aptamers are single stranded DNA, RNA or peptide sequences having the ability to bind a variety of specific targets (proteins, molecules as well as ions). Therefore, aptamer production and selection for therapeutic and diagnostic…
Whole-cell modelling is constrained by the laws of nature in general and the laws of thermodynamics in particular. This paper shows how one prolific source of information, stoichiometric models of biomolecular systems, can be integrated…